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Clinical Genetics

Evidence for the founder effect of a novel ACVRL1 splice-site mutation in Hungarian hereditary hemorrhagic telangiectasia families

T. Major, R. Gindele, Z. Szabó, T. Alef, B. Thiele, L. Bora, Z. Kis, P. Bárdossy, T. Rácz, I. Havacs, Z. Bereczky · Monday, June 13, 2016, 7:38

Tags: Genetics

American Journal of Medical Genetics Part A

A de novo microtriplication at 4q21.21-q21.22 in a patient with a vascular malignant hemangioma, elongated sigmoid colon, developmental delay, and absence of speech

Igor N. Lebedev, Lyudmila P. Nazarenko, Nikolay A. Skryabin, Nadezhda P. Babushkina, Anna A. Kashevarova · Saturday, June 11, 2016, 9:53

The widespread application of array comparative genomic hybridization (aCGH) has provided new insights into the clinical significance of copy number variations (CNVs) in the human genome. Many microdeletion syndromes have recently been linked to corresponding reciprocal microduplication syndromes related to CNVs in the same chromosomal regions. However, the extent of CNVs may not be restricted to only microduplications but may also include microtriplications or even quadruplications. 4q21 microdeletion syndrome is one of these recently described syndromes. The phenotype includes growth restriction, neonatal hypotonia, severe developmental delay, absent or delayed speech, and distinct facial features. The minimal critical deleted region, which is 1.3 Mb in size, contains the PRKG2, RASGEF1B, HNRNPD, HNRPDL, and ENOPH1genes. Here, we report a 5.4-year-old girl with developmental delay, absence of speech, muscular hypertension, macrocephaly, a broad forehead, frontal bossing, relatively elongated extremities, a vascular malignant hemangioma in anamnesis, and elongated sigmoid colon. aCGH revealed a microtriplication at 4q21.21-q21.22 that was 1.61 Mb in size. This de novo microtriplication included nine genes (BMP3, PRKG2, RASGEF1B,HNRNPD, HNRPDL, ENOPH1, TMEM150C, LINC00575, and SCD5) and overlapped with the minimal critical region for 4q21 microdeletion syndrome. Some clinical features of the patient were similar to those of 4q21 microdeletion (macrocephaly, frontal bossing, developmental delay, absence of speech, and anxiety), whereas others were mirrored (elongated extremities and muscular hypertension). The first identified case of a de novo microtriplication at 4q21.21-q21.22 emphasizes the clinical significance of CNVs at 4q21 for patients with developmental delay and absence of speech. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Van der Woude and Popliteal Pterygium Syndromes: Broad intrafamilial variability in a three generation family with mutation in IRF6

Andreas Busche, Ute Hehr, Peter Sieg, Gabriele Gillessen-kaesbach · Saturday, June 11, 2016, 9:53

Patients with Van der Woude syndrome typically present with cleft lip, cleft lip and palate, or with cleft palate only. In contrast to non-syndromic cleft lip and/or palate, Van der Woude syndrome typically is characterized by bilateral, paramedian lower-lip pits. Popliteal pterygium syndrome shares features with Van der Woude syndrome, but, in addition, is characterized by a popliteal pterygium, genital anomalies, cutaneous syndactyly of the fingers and the toes, and a characteristic pyramidal fold of skin overlying the nail of the hallux. In some patients oral synechiae or eyelid synechiae are present. Van der Woude Syndrome and Popliteal pterygium syndrome are autosomal dominantly inherited disorders caused by heterozygous mutations in IRF6. We present a three generation family with tremendous intrafamilial phenotypic variability. The newborn index patient had a diagnosis of Popliteal pterygium syndrome. The mother presented with a classic Van der Woude Syndrome, while the maternal grandfather had Van der Woude Syndrome as well as minor signs of Popliteal pterygium syndrome. In all three affecteds the known pathogenic mutation c.265A>G, p.Lys89Glu in IRF6 was identified. While inter- as well as intra-familial variability has been described in IRF6-related disorders, the occurrence of a typical Van der Woude Syndrome without any other anomalies as well as a diagnosis of Popliteal pterygium syndrome in the same family is rare. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions

Weimin Bi, Sau-wai Cheung, Amy M. Breman, Carlos A. Bacino · Saturday, June 11, 2016, 9:53

Deletions in the 4p16.3 region cause Wolf–Hirschhorn syndrome, a well known contiguous microdeletion syndrome with the critical region for common phenotype mapped in WHSCR2. Recently, duplications in 4p16.3 were reported in three patients with developmental delay and dysmorphic features. Through chromosomal microarray analysis, we identified 156 patients with a deletion (n = 109) or duplication (n = 47) in 4p16.3 out of approximately 60,000 patients analyzed by Baylor Miraca Genetics Laboratories. Seventy-five of the postnatally detected deletions encompassed the entire critical region, 32 (43%) of which were associated with other chromosome rearrangements, including six patients (8%) that had a duplication adjacent to the terminal deletion. Our data indicate that Wolf–Hirschhorn syndrome deletions with an adjacent duplication occur at a higher frequency than previously appreciated. Pure deletions (n = 14) or duplications (n = 15) without other copy number changes distal to or inside the WHSCR2 were identified for mapping of critical regions. Our data suggest that deletion of the segment from 0.6 to 0.9 Mb from the terminus of 4p causes a seizure phenotype and duplications of a region distal to the previously defined smallest region of overlap for 4p16.3 microduplication syndrome are associated with neurodevelopmental problems. We detected seven Wolf–Hirschhorn syndrome deletions and one 4p16.3 duplication prenatally; all of the seven are either >8 Mb in size and/or associated with large duplications. In conclusion, our study provides deeper insight into the molecular mechanisms, the critical regions and effective prenatal diagnosis for 4p16.3 deletions/ duplications. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Temporal changes in chromosome abnormalities in human spontaneous abortions: Results of 40 years of analysis

Kathy Hardy, Philip J. Hardy, Patricia A. Jacobs, Kevin Lewallen, Terry J. Hassold ·Saturday, June 11, 2016, 9:53

Studies during the past 50 years demonstrate the importance of chromosome abnormalities to the occurrence of early pregnancy loss in humans. Intriguingly, there appears to be considerable variation in the rates of chromosome abnormality, with more recent studies typically reporting higher levels than those reported in early studies of spontaneous abortions. We were interested in examining the basis for these differences and accordingly, we reviewed studies of spontaneous abortions conducted in our laboratories over a 40-year-time span. Our analyses confirm a higher rate of abnormality in more recent series of spontaneous abortions, but indicate that the effect is largely, if not entirely, attributable to changes over time in the maternal age structures of the study populations. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Genotype–phenotype correlation and pregnancy outcomes of partial trisomy 14q: A systematic review

Julia Bregand-white, Devereux N. Saller, Michele Clemens, Urvashi Surti, Svetlana A. Yatsenko, Aleksandar Rajkovic · Saturday, June 11, 2016, 9:53

Over the last decade, several advances in ultrasound techniques, increasing availability of whole genome microarray testing, and overall expansion of our knowledge about the human genome have drastically enhanced our ability to detect chromosomal abnormalities prenatally. Despite that, genotype–phenotype correlation is difficult to establish for many chromosomal aberrations, particularly for those that are rare, as it requires thorough analysis of a significant number of cases. This in turn increases the burden of the obstetric provider to appropriately counsel a patient regarding prognosis and pregnancy options in these complicated situations. Our experience in prenatal diagnosis and management of a fetus with multiple anomalies and partial trisomy for the 14q11–q24.2 prompted a comprehensive analysis of the relevant literature. Although complete non-mosaic trisomy 14 is associated with first trimester miscarriages, partial trisomy 14q is a rare condition with undefined genotype–phenotype correlation, preventing accurate prenatal counseling, and informed decision making. We performed a systematic literature review, that aimed to summarize prenatal and postnatal findings of individual case reports on 51 patients with partial trisomy 14q in order to elucidate genotype–phenotype correlation, and to supply healthcare professionals with recommendation on essential fetal and parental testing for accurate diagnosis, pregnancy outcomes, and proper family counseling. Comparison of the clinical findings among the patients with partial 14q trisomy suggest that the resulting phenotype is likely to be influenced by the extent of the 14q trisomy segment, associated chromosomal imbalances, parental origin of the rearrangement, and dosage of the genes within the imprinted 14q32 cluster. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

Clinical Genetics

Expanding non-invasive prenatal testing beyond chromosomes 21, 18, 13, X and Y

Peter Benn · Friday, June 10, 2016, 15:26

Abstract

Non-invasive prenatal testing (NIPT) based on cell-free DNA in maternal plasma is being expanded to include additional chromosome abnormalities beyond those involving chromosomes 21, 18, 13, X and Y. Review of population cytogenetic data provides insight into the likely number of additional abnormalities detectable. Additional clinically significant and cytogenetically recognizable abnormalities are present in less than 0.1% of newborns but clinically significant, or potentially significant, sub-microscopic imbalances are expected to be present in 1.7%. Cytogenetic studies on chorionic villus samples suggests that after excluding abnormalities involving chromosomes 21, 18, 13, X and Y, approximately 0.6% of NIPT results may be positive for an unbalanced abnormality attributable to mosaicism but most of these will not be confirmed at amniocentesis or in newborns. NIPT has also been developed for specific microdeletion syndromes and initial experience is now available. Laboratory procedures such as deeper sequencing and additional data analytics are rapidly evolving but even with existing protocols, it is already clear that NIPT does not necessarily need to be limited to trisomies 21, 18, 13 and the sex chromosome abnormalities. Patient educational materials and genetic counselling services need to be available for women offered expanded NIPT.

Tags: Genetics

American Journal of Medical Genetics Part A

BRAT1 mutations present with a spectrum of clinical severity

Siddharth Srivastava, Heather E. Olson, Julie S. Cohen, Cynthia S. Gubbels, Sharyn Lincoln, Brigette Tippin Davis, Layla Shahmirzadi, Siddharth Gupta, Jonathan Picker, Timothy W. Yu, David T. Miller, Janet S. Soul, Andrea Poretti, Sakkubai Naidu · Friday, June 10, 2016, 7:30

Mutations in BRAT1, encoding BRCA1-associated ATM activator 1, are associated with a severe phenotype known as rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL; OMIM # 614498), characterized by intractable seizures, hypertonia, autonomic instability, and early death. We expand the phenotypic spectrum of BRAT1 related disorders by reporting on four individuals with various BRAT1 mutations resulting in clinical severity that is either mild or moderate compared to the severe phenotype seen in RMFSL. Representing mild severity are three individuals (Patients 1–3), who are girls (including two sisters, Patients 1–2) between 4 and 10 years old, with subtle dysmorphisms, intellectual disability, ataxia or dyspraxia, and cerebellar atrophy on brain MRI; additionally, Patient 3 has well-controlled epilepsy and microcephaly. Representing moderate severity is a 15-month-old boy (Patient 4) with severe global developmental delay, refractory epilepsy, microcephaly, spasticity, hyperkinetic movements, dysautonomia, and chronic lung disease. In contrast to RMFSL, his seizure onset occurred later at 4 months of age, and he is still alive. All four of the individuals have compound heterozygous BRAT1 mutations discovered via whole exome sequencing: c.638dupA (p.Val214Glyfs*189); c.803+1G>C (splice site mutation) in Patients 1–2; c.638dupA (p.Val214Glyfs*189); c.419T>C (p.Leu140Pro) in Patient 3; and c.171delG (p.Glu57Aspfs*7); c.419T>C (p.Leu140Pro) in Patient 4. Only the c.638dupA (p.Val214Glyfs*189) mutation has been previously reported in association with RMFSL. These patients illustrate that, compared with RMFSL, BRAT1 mutations can result in both moderately severe presentations evident by later-onset epilepsy and survival past infancy, as well as milder presentations that include intellectual disability, ataxia/dyspraxia, and cerebellar atrophy. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Deletion 2q37 syndrome: Cognitive-behavioral trajectories and autistic features related to breakpoint and deletion size

Gene S. Fisch, Rena E. Falk, John C. Carey, Jaime Imitola, Maria Sederberg, Karen S. Caravalho, Sarah South · Friday, June 10, 2016, 7:30

Subtelomeric deletions have been reported in ∼2.5% of individuals with developmental disabilities. Subtelomeric deletion 2q37 has been detected in many individuals diagnosed with intellectual disabilities (ID) and autism spectrum disorders (ASD). Previously, genotype–phenotype correspondences were examined for their relationship to breakpoints 37.1, 37.2, or 37.3. Our purpose was to ascertain whether there were phenotypic differences at these breakpoints, elucidate the cognitive-behavioral phenotype in del2q37, and examine the genotype–phenotype association in the deletion with respect to cognitive-behavioral profiles and ASD. We administered a comprehensive cognitive-behavioral battery to nine children diagnosed with del 2q37, ages 3.9–17.75 years. ID for five tested with the Stanford–Binet (4th Edition) (SBFE) ranged from severe to mild [IQ Range: 36–59]. Adaptive behavior scores from the Vineland Adaptive Behavior Scale (VABS) were much below adequate levels (DQ Range: floor value ["19"] to 55). Autism scores from the Child Autism Rating Scale (CARS) ranged from 22 [non-autistic] to 56 [extremely autistic]; 5/8 [63%] children received scores on the autism spectrum. Participants with the largest deletions, 10.1 and 9.5 Mb, attained the highest IQ and DQ scores while those with the smallest deletions, 7.9 and 6.6 Mb, made the lowest IQ and DQ scores. No association between deletion breakpoint and phenotype were found. Assessment of the various deleted regions suggested histone deacetylase 4 gene (HDAC4) was a likely candidate gene for ASD in our sample. However, two earlier reports found no association between HDAC4 haploinsufficiency and ASD. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

BRAT1 mutations are associated with infantile epileptic encephalopathy, mitochondrial dysfunction, and survival into childhood

Denise Horn, Bernhard Weschke, Ellen Knierim, Björn Fischer-zirnsak, Werner Stenzel, Markus Schuelke, Tomasz Zemojtel · Friday, June 10, 2016, 7:30

We describe two siblings who were affected with early onset focal seizures, severe progressive postnatal microcephaly, muscular hypertonia, feeding problems and bouts of apnea, only minimal psychomotor development, as well as death in infancy and childhood. We identified compound heterozygous mutations in BRAT1 exons 5 (c.638_639insA) and 8 (c.1134+1G>A) in one affected child via next-generation sequencing of the disease-associated genome followed by phenotype-driven bioinformatic analysis. Sanger sequencing confirmed the presence of these mutations in both patients and a heterozygote status of the parents. Whereas the frameshift mutation (c.638_639insA) has been described in one family, the splice-site mutation (c.1134+1G>A) is novel. In contrast to all cases published so far, one of our patients showed a considerably milder clinical course with survival into childhood. Investigation of a skeletal muscle biopsy showed a severely reduced COX enzyme histochemical staining, indicating mitochondrial dysfunction. Our data expand the clinical and mutational spectrum of the BRAT1-associated phenotype. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

Clinical Genetics

Issue Information - Editorial Board

Friday, June 10, 2016, 7:26

Tags: Genetics

Clinical Genetics

IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families

E.j. Leslie, D.c. Koboldt, C.j. Kang, L. Ma, J.t. Hecht, G.l. Wehby, K. Christensen, A.e. Czeizel, F.w.-b. Deleyiannis, R.s. Fulton, R.k. Wilson, T.h. Beaty, B.c. Schutte, J.c. Murray, M.l. Marazita · Friday, June 10, 2016, 7:26

Van der Woude syndrome (VWS) is an autosomal dominant malformation syndrome characterized by orofacial clefting (OFC) and lower lip pits. The clinical presentation of VWS is variable and can present as an isolated OFC, making it difficult to distinguish VWS cases from individuals with non-syndromic OFCs. About 70% of causal VWS mutations occur in IRF6, a gene that is also associated with non-syndromic OFCs. Screening for IRF6 mutations in apparently non-syndromic cases has been performed in several modestly sized cohorts with mixed results. In this study, we screened 1521 trios with presumed non-syndromic OFCs to determine the frequency of causal IRF6mutations. We identified seven likely causal IRF6 mutations, although a posteriori review identified two misdiagnosed VWS families based on the presence of lip pits. We found no evidence for association between rare IRF6 polymorphisms and non-syndromic OFCs. We combined our results with other similar studies (totaling 2472 families) and conclude that causal IRF6 mutations are found in 0.24–0.44% of apparently non-syndromic OFC families. We suggest that clinical mutation screening for IRF6 be considered for certain family patterns such as families with mixed types of OFCs and/or autosomal dominant transmission.

Tags: Genetics

Clinical Genetics

JP–HHT phenotype in Danish patients with SMAD4 mutations

A. M. Jelsig, P. M. Tørring, A. D. Kjeldsen, N. Qvist, A. Bojesen, U. B. Jensen, M. K. Andersen, A. M. Gerdes, K. Brusgaard, L. B. Ousager · Friday, June 10, 2016, 7:26

Patients with germline mutations in SMAD4 can present symptoms of both juvenile polyposis syndrome (JPS) and hereditary hemorrhagic telangiectasia (HHT): the JP-HHT syndrome. The complete phenotypic picture of this syndrome is only just emerging. We describe the clinical characteristics of 14 patients with SMAD4-mutations. The study was a retrospective, register-based study. SMAD4 mutations carriers were identified through the Danish HHT-registry, the genetic laboratories – and the genetic departments in Denmark. The medical files from relevant departments were reviewed and symptoms of HHT, JPS, aortopathy and family history were noted. We detected 14 patients withSMAD4 mutations. All patients had polyps removed and 11 of 14 fulfilled the diagnostic criteria for JPS. Eight patients were screened for HHT-symptoms and seven of these fulfilled the Curaçao criteria. One patient had aortic root dilation. Our findings support that SMAD4 mutations carriers have symptoms of both HHT and JPS and that the frequency of PAVM and gastric involvement with polyps is higher than in patients with HHT or JPS not caused by a SMAD4 mutation. Out of eight patients screened for aortopathy, one had aortic root dilatation, highlighting the need for additional screening for aortopathy.

Tags: Genetics

Clinical Genetics

A novel CHST3 allele associated with spondyloepiphyseal dysplasia and hearing loss in Pakistani kindred

A. M. Waryah, M. Shahzad, H. Shaikh, S. A. Sheikh, N. A. Channa, R. B. Hufnagel, A. Makhdoom, S. Riazuddin, Z. M. Ahmed · Friday, June 10, 2016, 7:26

Skeletal dysplasias (SDs) are highly heterogeneous disorders composed of 40 clinical sub-types that are part of 456 well-delineated syndromes in humans. Here, we enrolled consanguineous kindred from a remote area of Sindh province of Pakistan, with 14 affected individuals suffering with short stature, kyphoscoliosis, joint dislocations, clubfoot, heart valve anomalies and progressive bilateral mixed hearing loss. To identify pathogenic variants in this family, whole exome sequencing (WES) was performed in one affected and one normal individual, which revealed a novel transversion mutation (c.802G>T; p.Glu268*) in CHST3 associated with the phenotype. CHST3 encodes a chondroitin 6-O-sulfotransferase-1 (C6ST-1) enzyme that is essential for the sulfation of proteoglycans found in cartilages. Previously, mutations in CHST3 have largely been reported in sporadic cases of SD, primarily with severe spinal abnormalities, joint dislocations, joint contractures, and clubfoot. Clinical and radiological examination of the affected individuals in this family provides new insights into phenotypic spectrum ofCHST3 alleles and disease progression with age.

Tags: Genetics

G3: .Genes, Genomes, Genetics Mission - Online First Articles

Synthetic Physical Interactions Map Kinetochore-Checkpoint Activation Regions

Olafsson, G., Thorpe, P. H. · Thursday, June 09, 2016, 23:26

The spindle assembly checkpoint (SAC) is a key mechanism to regulate the timing of mitosis and ensure that chromosomes are correctly segregated to daughter cells. The recruitment of the Mad1 and Mad2 proteins to the kinetochore is normally necessary for SAC activation. This recruitment is coordinated by the SAC kinase Mps1, which phosphorylates residues at the kinetochore to facilitate binding of Bub1, Bub3, Mad1 and Mad2. There is evidence that the essential function of Mps1 is to direct recruitment of Mad1/2. To test this model we have systematically recruited Mad1, Mad2 and Mps1 to most proteins in the yeast kinetochore and find that while Mps1 is sufficient for checkpoint activation, recruitment of either Mad1 or Mad2 is not. These data indicate an important role for Mps1 phosphorylation in SAC activation, beyond the direct recruitment of Mad1 and Mad2.

Tags: Genetics

G3: .Genes, Genomes, Genetics Mission - Online First Articles

Identification of Functional Domains in the Cohesin Loader Subunit Scc4 by a Random Insertion/Dominant Negative Screen

Shwartz, M., Matityahu, A., Onn, I. · Thursday, June 09, 2016, 23:26

Cohesin is a multi-subunit complex that plays an essential role in genome stability. Initial association of cohesin with chromosomes requires the loader, a heterodimer composed of Scc4 and Scc2. However, very little is known about the loader's mechanism of action. In this study we performed a genetic screen to identify functional domains in the Scc4 subunit of the loader. We isolated scc4 mutant alleles that when overexpressed have a dominant negative effect on cell viability. We defined a small region in the N' terminal of Scc4 that is dominant negative when overexpressed, and on which Scc2/4 activity depends. When the mutant alleles are expressed as a single copy, they are recessive and do not support cell viability, cohesion, cohesin loading or Scc4 chromatin binding. In addition, we show that the mutants investigated reduce but do not eliminate the interaction of Scc4 with either Scc2 or cohesin. However, we show that Scc4 cannot bind cohesin in the absence of Scc2. Our results provide new insight into the roles of Scc4 in cohesin loading and contribute to the deciphering of the loading mechanism.

Tags: Genetics

G3: .Genes, Genomes, Genetics Mission - Online First Articles

A Genetic Screen for Mutants with Supersized Lipid Droplets in Caenorhabditis elegans

Li, S., Xu, S., Ma, Y., Wu, S., Feng, Y., Cui, Q., Chen, L., Zhou, S., Kong, Y., Zhang, X., Yu, J., Wu, M., Zhang, S. O. · Thursday, June 09, 2016, 23:26

To identify genes that regulate the dynamics of lipid droplet (LD) size, we have used the genetically tractable model organism Caenorhabditis elegans, whose wild-type LD population displays a steady state of size with an upper limit of 3 μm in diameter. From a saturated forward genetic screen of 6.7 x 10⁵ mutagenized haploid genomes, we isolated 118 mutants with supersized intestinal LDs often reaching 10 μm. These mutants define nine novel complementation groups, in addition to four known genes (maoc-1, dhs-28, daf-22 & prx-10). The nine groups are named drop (lipid droplet abnormal) and categorized into four classes. Class I mutants drop-5 & drop-9, similar to prx-10, are up-regulated in ACS-22-DGAT-2-dependent LD growth, resistant to LD hydrolysis, and defective in peroxisome import. Class II mutants drop-2, drop-3, drop-6 & drop-7, are up-regulated in LD growth, resistant to LD hydrolysis, but not defective in peroxisome import. Class III mutants drop-1 & drop-8 are neither up-regulated in LD growth nor resistant to LD hydrolysis, but seemingly up-regulated in LD fusion. Class IV mutantdrop-4 is cloned as sams-1 and, different to the other three classes, is ACS-22-independent and hydrolysis-resistant. These four classes of supersized LD mutants should be valuable for mechanistic studies of LD cellular processes including growth, hydrolysis, and fusion.

Tags: Genetics

G3: .Genes, Genomes, Genetics Mission - Online First Articles

A Combination of CRISPR/Cas9 and Standardized RNAi as a Versatile Platform for the Characterization of Gene Function

Wissel, S., Kieser, A., Yasugi, T., Duchek, P., Roitinger, E., Gokcezade, J. F., Steinmann, V., Gaul, U., Mechtler, K., Forstemann, K., Knoblich, J. A., Neumuller, R. A. · Thursday, June 09, 2016, 23:26

Traditional loss-of-function studies in Drosophila suffer from a number of shortcomings including off-target effects in the case of RNA interference (RNAi) or the stochastic nature of mosaic clonal analysis. Here, we describe minimal in vivo GFP interference (miGFPi) as a versatile strategy to characterize gene function and to conduct highly stringent, cell-type specific loss-of-function experiments in Drosophila. miGFPi combines CRISPR/Cas9 mediated tagging of genes at their endogenous locus with an immunotag and an exogenous 21 nucleotide RNAi effector sequence with the use of a single reagent, highly validated RNAi line targeting this sequence. We demonstrate the utility and time effectiveness of this method by characterizing the function of the Polymerase I (Pol I) associated transcription factor Tif-1a and the previously uncharacterized geneMESR4 in the Drosophila female germline stem cell lineage. In addition, we show thatmiGFPi serves as a powerful technique to functionally characterize individual isoforms of a gene. We exemplify this aspect of miGFPi by studying isoform specific loss-of-function phenotypes of the longitudinals lacking (lola) gene in neural stem cells. Altogether, themiGFPi strategy constitutes a generalized loss-of-function approach that is amenable to study the function of all genes in the genome in a stringent and highly time effective manner.

Tags: Genetics

Clinical Genetics

Association of a Type 2 Diabetes Genetic Risk Score with Insulin Secretion Modulated by Insulin Sensitivity among Chinese Hans

Xiaomu Kong, Xiaoyan Xing, Jing Hong, Xuelian Zhang, Wenying Yang · Thursday, June 09, 2016, 19:24

Abstract

Type 2 diabetes (T2D) is characterized by insulin resistance and impaired insulin secretion. The present study aimed to identify the influence of insulin sensitivity on the genetic risk of impaired insulin secretion among a Chinese Han population. For 3,229 controls and 1,994 treatment naïve T2D, single nucleotide polymorphisms (SNPs) from 24 T2D-related genomic loci were genotyped and a genetic risk score (GRS) was constructed. Results showed that GRS was associated with insulin secretion and disposition indices in both controls and treatment naïve T2Ds. Upon stratifying the participants into tertiles by the Matsuda index, we observed an inhibitory relationship between the GRS and insulin secretion in low insulin sensitive but not in high insulin sensitive controls and treatment naïve T2Ds. Moreover, low insulin sensitive individuals exhibited more severe impairment in insulin secretion and beta cell response to insulin sensitivity with an increase in risk alleles. Our findings identified that the association of GRS with insulin secretion was strongly modulated by insulin sensitivity in both controls and T2Ds of Chinese Han. It indicates that insulin sensitization should be emphasized in prevention and treatment of T2D for beta cell protection.

The present study aimed to identify the influence of insulin sensitivity on the genetic risk of impaired insulin secretion among a Chinese Han population. Results showed that GRS was associated with insulin secretion and disposition indices in both controls and treatment naive type 2 diabetes (T2D) patients. Upon stratifying the participants into tertiles by the Matsuda index, we observed an inhibitory relationship between the GRS and insulin secretion in low insulin sensitive but not in high insulin sensitive controls and treatment naive T2Ds. Low insulin sensitive individuals exhibited more severe impaiinient in insulin secretion and beta cell response to insulin sensitivity with an increase in risk alleles. It indicates that insulin sensitization should be emphasized in prevention and treatment of T2D for beta cell protection in Chinese Hans.

Tags: Genetics

American Journal of Medical Genetics Part A

Deletion upstream of SALL1 producing Townes–Brocks syndrome

Cathy A. Stevens, Kristin M. May · Thursday, June 09, 2016, 9:27

Tags: Genetics

American Journal of Medical Genetics Part A

RIN2 syndrome: Expanding the clinical phenotype

Simonetta Rosato, Delfien Syx, Ivan Ivanovski, Marzia Pollazzon, Daniela Santodirocco, Loredana De Marco, Marina Beltrami, Bert Callewaert, Livia Garavelli, Fransiska Malfait ·Thursday, June 09, 2016, 9:27

Biallelic defects in the RIN2 gene, encoding the Ras and Rab interactor 2 protein, are associated with a rare autosomal recessive connective tissue disorder, with only nine patients from four independent families reported to date. The condition was initially termed MACS syndrome (macrocephaly, alopecia, cutis laxa, and scoliosis), based on the clinical features of the first identified family; however, with the expansion of the clinical phenotype in additional families, it was subsequently coined RIN2 syndrome. Hallmark features of this condition include dysmorphic facial features with striking, progressive facial coarsening, sparse hair, normal to enlarged occipitofrontal circumference, soft redundant and/or hyperextensible skin, and scoliosis. Patients with RIN2 syndrome present phenotypic overlap with other conditions, including EDS (especially the dermatosparaxis and kyphoscoliosis subtypes). Here, we describe a 10th patient, the first patient of Caucasian origin and the oldest reported patient so far, who harbors the previously identified homozygous RIN2 mutation c.1878dupC (p. (Ile627Hisfs*7)). Besides the hallmark features, this patient also presents problems not previously associated with RIN2 syndrome, including cervical vertebral fusion, mild hearing loss, and colonic fibrosis. We provide an overview of the clinical findings in all reported patients with RIN2 mutations and summarize some of the possible pathogenic mechanisms that may underlie this condition. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

Gene Expression Patterns

An in situ hybridization study of Hyaluronan synthase (Has) mRNA in developing mouse molar and incisor tooth germs

Wednesday, June 08, 2016, 23:31

Publication date: Available online 8 June 2016
Source:Gene Expression Patterns
Author(s): Tsuyoshi Morita, Kaoru Fujikawa, Otto Baba, Shunichi Shibata
Hyaluronan (HA) is a major constituent molecule in most extracellular matrices and is synthesized by Hyaluronan synthase (Has). In the present study, we examined expression patterns of Has1, -2, -3 mRNA in developing mouse molar and incisor tooth germs from embryonic day (E) 11.5 to postnatal day (P) 7, focusing on Hertwig's epithelial root sheath (HERS) and the apical bud in particular. Has1 mRNA expression was not detected in all tooth germs examined. Has2 mRNA was expressed in the surrounding mesenchyme from E12.0 to 18.0 in both molar and incisor tooth germs, but disappeared after birth. Meanwhile, Has3 mRNA was exclusively expressed within the enamel organ, especially in the inner enamel epithelium (IEE), stellate reticulum (SR), and stratum intermedium (SI) until the early bell stage at E16.0. Has3 mRNA disappeared as IEE differentiated into differentiating ameloblasts (dABs), but remained in SI until the root developmental stage of the molar tooth germ at P7. Has3 mRNA was also expressed in HERS until P7. In incisors, Has3 mRNA was expressed in the apical bud, especially in the transit-amplifying (TA) cell region from E16.0 to P7, and in the papillary layer (PL) adjacent to the mature enamel. These gene expression patterns suggested that Has3 is the main control factor for prenatal and postnatal HA synthesis of the tooth germ, and may in part regulate crown and root formation of the tooth germ, maintenance of stem cell niches in the apical bud as well as mineral transport in PL. 

Tags: Genetics

Human Genetics

Genome editing and the next generation of antiviral therapy

Wednesday, June 08, 2016, 23:05

Abstract

Engineered endonucleases such as homing endonucleases (HEs), zinc finger nucleases (ZFNs), Tal-effector nucleases (TALENS) and the RNA-guided engineered nucleases (RGENs or CRISPR/Cas9) can target specific DNA sequences for cleavage, and are proving to be valuable tools for gene editing. Recently engineered endonucleases have shown great promise as therapeutics for the treatment of genetic disease and infectious pathogens. In this review, we discuss recent efforts to use the HE, ZFN, TALEN and CRISPR/Cas9 gene-editing platforms as antiviral therapeutics. We also discuss the obstacles facing gene-editing antiviral therapeutics as they are tested in animal models of disease and transition towards human application.

Tags: Genetics

American Journal of Medical Genetics Part A

Etiologies of uterine malformations

Adeline Jacquinet, Debra Millar, Anna Lehman · Wednesday, June 08, 2016, 9:25

Ranging from aplastic uterus (including Mayer–Rokitansky–Kuster–Hauser syndrome) to incomplete septate uterus, uterine malformations as a group are relatively frequent in the general population. Specific causes remain largely unknown. Although most occurrences ostensibly seem sporadic, familial recurrences have been observed, which strongly implicate genetic factors. Through the study of animal models, human syndromes, and structural chromosomal variation, several candidate genes have been proposed and subsequently tested with targeted methods in series of individuals with isolated, non-isolated, or syndromic uterine malformations. To date, a few genes have garnered strong evidence of causality, mainly in syndromic presentations (HNF1B, WNT4, WNT7A,HOXA13). Sequencing of candidate genes in series of individuals with isolated uterine abnormalities has been able to suggest an association for several genes, but confirmation of a strong causative effect is still lacking for the majority of them. We review the current state of knowledge about the developmental origins of uterine malformations, with a focus on the genetic variants that have been implicated or associated with these conditions in humans, and we discuss potential reasons for the high rate of negative results. The evidence for various environmental and epigenetic factors is also reviewed. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Urorectal septum malformation sequence—Fetal series with the description of a new "intermediate" variant. Time to refine the terminology?

Kuan-ying Huang, Kuan-ting Kuo, Yi-ping Li, Ming Chen, Ching-uen Yu, Jin-chung Shih ·Wednesday, June 08, 2016, 9:25

Tags: Genetics

American Journal of Medical Genetics Part A

Chronic intestinal pseudo-obstruction in a child harboring a founder Hirschsprung RET mutation

Valentina Rossi, Manuela Mosconi, Paolo Nozza, Daniele Murgia, Girolamo Mattioli, Isabella Ceccherini, Alessio Pini Prato · Wednesday, June 08, 2016, 9:25

Chronic intestinal pseudo obstruction (CIPO) is a rare clinical entity characterized by symptoms and signs of intestinal obstruction without either recognizable anatomical abnormalities or intestinal aganglionosis. A Chinese female infant presented to our institution with a clinical diagnosis of CIPO. Aganglionosis was ruled out by full thickness colonic and ileal biopsies and by rectal suction biopsies. Unexpectedly, direct sequencing and PCR amplification of RET proto-oncogene from peripheral blood extracted DNA identified a RET R114H mutation. This mutation has already been reported as strongly associated with Asian patients affected by Hirschsprung's disease (HSCR) and is considered a founder mutation in Asia. The same mutation has never been reported in patients with CIPO, so far. These findings support the role of RET in the development of the enteric nervous system but underline the importance of other genetic or environmental factors contributing to the gastrointestinal phenotype of the disease. Somehow, this RET R114H mutation proved to have a role in the etiology of both CIPO and HSCR and could contribute to a more diffuse imbalance of gut dysmotility. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Homozygous deletion of exons 2 and 3 of NPC2 associated with Niemann–Pick disease type C

Malavika Hebbar, Harsha Prasada L, Aneek Das Bhowmik, Daniel Trujillano, Anju Shukla, Shrijeet Chakraborti, Krishna Kumar Kandaswamy, Arndt Rolfs, Nutan Kamath, Ashwin Dalal, Stephanie Bielas, Katta Mohan Girisha · Wednesday, June 08, 2016, 9:25

Tags: Genetics

American Journal of Medical Genetics Part A

Is one diagnosis the whole story? patients with double diagnoses

Alina Kurolap, Naama Orenstein, Inbal Kedar, Monika Weisz Hubshman, Dov Tiosano, Adi Mory, Zohar Levi, Daphna Marom, Lior Cohen, Nina Ekhilevich, Jessica Douglas, Catherine Bearce Nowak, Wen-hann Tan, Hagit N. Baris · Wednesday, June 08, 2016, 9:25

One of the goals of evaluating a patient in the genetics clinic is to find the diagnosis that would explain his or her clinical presentation. Sometimes the patient's diagnosis remains undefined or does not explain all of the clinical findings. As clinicians are often guided by a "single disorder" paradigm, diagnosing multiple genetic conditions in the same patient requires a heightened sense of awareness. Over the last few years, we evaluated several patients (n = 14) who were found to have more than one genetic diagnosis. In this paper, we will describe their natural history and diagnoses, and draw on the lessons learned from this phenomenon, which we expect to grow in this era of next-generation diagnostic technologies. To our knowledge, this is by far the largest series of patients with double diagnoses. Based on our findings, we strongly recommend that physicians question every diagnosis to determine whether it indeed explains all of the patients' symptoms, and consider whether they should continue the diagnostic evaluation to look for a more accurate and complete set of diagnoses. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Quality of life, unmet needs, and iatrogenic injuries in rehabilitation of patients with Ehlers–Danlos Syndrome hypermobility type/Joint Hypermobility Syndrome

Claire Bovet, Matthew Carlson, Matthew Taylor · Wednesday, June 08, 2016, 9:25

Ehlers–Danlos Syndrome, hypermobility type (EDS-HT) and the joint hypermobility syndrome (JHS) are connective tissue disorders that form an overlapping clinical syndrome and are associated with frequent medical visits and substantial morbidity. EDS-HT/JHS-associated pain correlates with poor quality of life. While physical therapy is the recommended treatment for EDS-HT/JHS, little is known about therapy-related patient experiences and iatrogenic injuries. We studied 38 adult EDS-HT/JHS patients, eliciting health-related quality of life (HRQoL) from 28 patients through the RAND SF-36 questionnaire. We also explored physical therapy experiences through focus groups with 13 patients. Our patients displayed poor HRQoL, with 71% reporting worse health over the past year. SF-36 scores were significantly lower than the scores of the average American population (P < 0.001 for 8 of 10 categories assessed), but were comparable to EDS-HT/JHS populations in Belgium, the Netherlands, Sweden, and Italy. Focus groups identified factors associated with: negative past physical therapy experiences, iatrogenic joint injuries, positive treatment experiences, and unmet rehabilitation needs. This group of EDS-HT/JHS patients has significant decrements in HRQoL and many unmet treatment needs, as well as a risk for iatrogenic injuries. We identify several approaches to help meet patients' needs and improve joint rehabilitation in patients with EDS-HT/JHS. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

American Journal of Medical Genetics Part A

Quality of life in adolescents and adults with CHARGE syndrome

Nancy Hartshorne, Alexandra Hudson, Jillian Maccuspie, Benjamin Kennert, Tasha Nacarato, Timothy Hartshorne, Kim Blake · Wednesday, June 08, 2016, 9:25

Health-related Quality of Life and the Impact of Childhood Neurologic Disability Scale were collected for 53 patients with CHARGE syndrome aged 13–39 years with a mean academic level of 4th grade. The most prevalent new and ongoing issues included bone health issues, sleep apnea, retinal detachment, anxiety, and aggression. Sleep issues were significantly correlated with anxiety, self-abuse, conduct problems, and autistic-like behaviors. Problems with overall health, behavior, and balance most affected the number of social activities in the individual's life. Sensory impairment most affected relationships with friends. Two contrasting case studies are presented and demonstrate that the quality of life exists on a broad spectrum in CHARGE syndrome, just as its physical features range from mild to very severe. A multitude of factors, including those beyond the physical manifestations, such as anxiety and sleep problems, influence quality of life and are important areas for intervention. © 2016 Wiley Periodicals, Inc.

Tags: Genetics

Human Genetics

De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features

Tuesday, June 07, 2016, 23:05

Abstract

Whole exome sequencing (WES) can be used to efficiently identify de novo genetic variants associated with genetically heterogeneous conditions including intellectual disabilities. We have performed WES for 4102 (1847 female; 2255 male) intellectual disability/developmental delay cases and we report five patients with a neurodevelopmental disorder associated with developmental delay, intellectual disability, behavioral problems, hypotonia, speech problems, microcephaly, pachygyria and dysmorphic features in whom we have identified de novo missense and canonical splice site mutations in CSNK2A1, the gene encoding CK2α, the catalytic subunit of protein kinase CK2, a ubiquitous serine/threonine kinase composed of two regulatory (β) and two catalytic (α and/or α′) subunits. Somatic mutations in CSNK2A1 have been implicated in various cancers; however, this is the first study to describe a human condition associated with germline mutations in any of the CK2 subunits.

Tags: Genetics

Human Genetics

A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition

Tuesday, June 07, 2016, 23:05

Abstract

Intellectual disability is a common and highly heterogeneous disorder etiologically. In a multiplex consanguineous family, we applied autozygosity mapping and exome sequencing and identified a novel homozygous truncating mutation in PUS3 that fully segregates with the intellectual disability phenotype. Consistent with the known role of Pus3 in isomerizing uracil to pseudouridine at positions 38 and 39 in tRNA, we found a significant reduction in this post-transcriptional modification of tRNA in patient cells. Our finding adds to a growing list of intellectual disability disorders that are caused by perturbation of various tRNA modifications, which highlights the sensitivity of the brain to these highly conserved processes.

Tags: Genetics

Human Genetics

A review of gigaxonin mutations in giant axonal neuropathy ( GAN ) and cancer

Tuesday, June 07, 2016, 23:05

Abstract

Gigaxonin, the product of GAN gene localized to chromosome 16, is associated with the early onset neuronal degeneration disease giant axonal neuropathy (GAN). Gigaxonin is an E3 ubiquitin ligase adaptor protein involved in intermediate filament processing in neural cells, and vimentin filaments in fibroblasts. Mutations of the gene cause pre-neural filaments to accumulate and form giant axons resulting in the inhibition of neural cell signaling. Analysis of the catalog of somatic mutations in cancer, driver DB and IDGC data portal databases containing 21,000 tumor genomic sequences has identified GANpatient mutations in cancer cell lines and primary tumors. The database search has also shown the presence of identical missense and nonsense gigaxonin mutations in GANand colon cancer. These mutations frequently occur in the domains associated with protein homodimerization and substrate interaction such as Broad-Complex, Tramtrack and Bric a brac (BTB), BTB associated C-terminal KELCH (BACK), and KELCH repeats. Analysis of the International HapMap Project database containing 1200 normal genomic sequences has identified a single nucleotide polymorphism (SNP), rs2608555, in exon 8 of the gigaxonin sequence. While this SNP is present in >40 % of Caucasian population, it is present in less than 10 % of Japanese and Chinese populations. Although the role of gigaxonin polymorphism is not yet known, CFTR and MDR1 gene studies have shown that silent mutations play a role in the instability and aberrant splicing and folding of mRNAs. We believe that molecular and functional investigation of gigaxonin mutations including the exon 8 polymorphism could lead to an improved understanding of the relationship between GAN and cancer.

Tags: Genetics

Human Genetics

FCGR3A and FCGR3B copy number variations are risk factors for sarcoidosis

Tuesday, June 07, 2016, 23:05

Abstract

Sarcoidosis is a multisystem granulomatous disorder that causes significant morbidity. Genetic factors contribute to sarcoidosis risks. In this study, we investigated whether copy number variations (CNVs) of FCGR3A (coding for FcγRIIIA) and FCGR3B (coding for FcγRIIIB) genes are associated with sarcoidosis susceptibility and whether the expressions of FcγRIIIA on NK cells and FcγRIIIB on neutrophils are altered in sarcoidosis patients. TaqMan real-time PCR assays were used to analyze the CNV of FCGR3A andFCGR3B genes. FCGR3A and FCGR3B CNV genotypes were compared between 671 biopsy-proven sarcoidosis patients and the same number of healthy controls matched with age, sex, race, and geographic area from the ACCESS (A Case Control Etiologic Study of Sarcoidosis) cohort. Flow cytometry analyses were used to determine expressions of FcγRIIIA on NK cells and FcγRIIIB on neutrophils in phenotype analyses. We found that FCGR3A CNVs were significantly associated with sarcoidosis in females (CN = 1 vs. CN = 2 logistic regression adjusted for sex and race, OR 4.0156, SE = 2.2784, P = 0.0143; CN = 3 vs. CN = 2 logistic regression adjusted for sex and race, OR 2.8044, SE = 1.1065, P = 0.0090), suggesting that FCGR3A gene abnormality influences sarcoidosis development in a gender-specific manner. Furthermore, FcγRIIIA expressions were significantly decreased on NK cells from sarcoidosis patients compared to those from healthy controls (P = 0.0007). Additionally, low FCGR3B CN was associated with sarcoidosis (CN <2 vs. CN = 2 logistic regression adjusted for sex and race, OR 1.5025, SE = 0.2682, P = 0.0226), indicating that the functions of FCGR3Bgene may also contribute to the pathogenesis of sarcoidosis. We conclude that FCGR3ACNVs are a major risk factor for female sarcoidosis and FCGR3B CNVs may also affect the development of sarcoidosis.

Tags: Genetics

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